The phyloseq R package and associated tools and documentation are provided free of charge and open-source, with the expectation that work derived from these materials will be properly cited and attributed. The following serves as useful examples of the articles one might cite, as well as additional links to documentation on phyloseq, its associated tools, and its theoretical motivations.

Shiny-phyloseq: a phyloseq GUI Web Application

Improved Normalization and Feature Detection

The phyloseq R package citation

McMurdie and Holmes (2013) phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PLoS ONE. 8(4):e61217

“Full Stack” Example Workflow

Callahan BJ, Sankaran K, Fukuyama JA et al. Bioconductor workflow for microbiome data analysis: from raw reads to community analyses F1000Research 2016, 5:1492